Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagattgtcagtcagagctgcttatcgctgaatttaatttcttcaaccaagttaatattgaacaattctgttgcag

Basic information

species Zea mays
transcript GRMZM2G106795_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106795_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g47110.3 (Oryza sativa), 5'ss of exon 3
----------------------------------------ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctg-tagattgtcagtcagagctgcttatcgctgaatttaatttcttcaaccaagttaatattgaacaattctgttgcag
                                        |||||||||||||||||||||||| | ||||| || |||||||| ||||| || |||||||| |  ||   | |   | ||   |||| |||    |  ||   || || |   ||| |||  ||       | ||||||||
CTTATTCCTATATGTTATTTTTGCACGTTCTGATTTGCAGATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCGGAGTTTCAGgtttaataagctattt-taagttatgctcatcagatagcttgccttgtt-agtgaagctaaggtttggtggctttgttgcag

upper sequence: GRMZM2G106795_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 5'ss of exon 4
ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctg-tagattgtcagtcagagctgcttatcgctgaatttaatttcttcaaccaagttaatattgaacaattctgttgcag
|||||||||||||||||||||||| | ||||| || |||||||| ||||| || |||||||| |  ||   | |   | ||   |||| |||    |  ||   || || |   ||| |||  ||       | ||||||||
ATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCGGAGTTTCAGgtttaataagctattt-taagttatgctcatcagatagcttgccttgtt-agtgaagctaaggtttggtggctttgttgcag

upper sequence: GRMZM2G106795_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 4
ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagattgtcagtcagagctgcttatcgctgaatttaatttcttcaa------ccaagttaatattgaacaattctg-ttgcag
|||||||| |||||||| |||||||| ||||||||||||||||| || || || |||||||| ||    |  |   | |    |   | ||       ||||||  || |       |  ||||| | ||    | ||||  || |||
ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgt-tgggtgtcctagataatgcatttatgtcaaacgtcttaattggttgattagtttctcagttagt-ttacttatttcttctttcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|74241061|gb|DT648975.1|DT648975
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
EST: gi|101398288|gb|EB821017.1|EB821017
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTTCCTGCTTAACAGTGTCATATTGGTATTTGCC
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
EST: gi|211076278|gb|FL377992.1|FL377992
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTTCATGCTTAACA
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACA
EST: gi|211066463|gb|FL305323.1|FL305323
EST:     TGATTCATTGGATCGGGAGAGGATTGGAAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATG
genomic: TGATTCATTGGATCGGGAGAGGATTGGAAAA-GCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATG
EST: gi|211497259|gb|FL426008.1|FL426008
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGAT
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGAT
EST: gi|211066466|gb|FL305326.1|FL305326
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTTCATGCTTAACAGTGTCATATTGGTATTTGCC
EST: gi|211066462|gb|FL305322.1|FL305322
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCCTTT
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCCTTT
EST: gi|211069202|gb|FL305332.1|FL305332
EST:     TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG                         GCAATAATCAATGATCC
genomic: TTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagat ... tctgttgcagGCAATAATCAATGATCC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagattgtcagtcagagctgcttatcgctgaatttaatttcttcaaccaagttaatattgaacaattctgttgcag

- - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - -  AGCTGA